How to not restart from beginning stages with automated workflows when adding new version

I feel like this is a basic question, but we are having an issue regarding adding new proofs. We have just implemented automated workflows and every time a person adds a new proof, the workflows starts from the beginning stage when in reality we only want the current or next stage in the process to be notified of the new version.

Is the solution just un-checking the "notify users via email" option when adding the new version? Or is there another way to do it? I feel like the answer is probably very obvious but can't seem to figure it out!